CDC Nowcast: BA.5 Still Dominant But Losing Ground To A Growing Array Of Subvariants

#17,062

BA.5 - which peaked with roughly (revised) 86% of cases in late August - remains the dominant strain (67.9%), but is under pressure from BA.4.6 (now just over 12%) of cases, BF.7 with 5.3% of cases, and two newcomers this week - BQ1.1 and BQ.1 - both at 5.7%.

It isn't clear whether any of these viral interlopers have what it takes to fully dislodge BA.5, but history has shown that Omicron variants tend to reign for only a few months before being supplanted, making BA.5 already a bit long in the tooth. 

At the same time, three other Omicron variants - BA.2.75.2, BA.275 and BA.4  - appear to be losing ground. 

There isn't a lot known about the potential impact of these two newcomers (BQ.1 & BQ.1.1), but Public Health Ontario has recently released a preliminary risk assessment (excerpt below). Both are sublineages of the BA.5 variant, with mutations K444T, L452R, N460K, and F486V in the spike protein. BQ.1.1 additionally contains the mutation R346T. 

Risk Assessment for Omicron Sublineages BQ.1and BQ.1.1 (as of Oct 5, 2022)

 Published: October 2022 

Key Messages

• The earliest documented sequences of the BA.5 sublineages BQ.1 and BQ.1.1 date from mid-July 2022 and have been reported in multiple countries including Nigeria, United Kingdom (UK), Japan, United States (US), France, Belgium, Denmark, and Italy. 1 As of October 3, 2022, there has been 12 documented cases of BQ.1.1 in Canada.2 As of October 7th, 2022, globally there are 326 sequences uploaded to GISAID.3 
• While BQ.1 and BQ.1.1 currently comprise a small proportion of all COVID-19 cases globally, in some settings the proportion of cases is increasing at a rate suggestive of increased transmissibility relative to other circulating variants.
• The convergence of spike protein mutations found in BQ.1 and BQ.1.1 are a concern and merit ongoing monitoring due to their potential to cause significant immune escape. 
• There is little evidence to inform the risks of BQ.1 and BQ.1.1 with respect to transmissibility, immune evasion, and disease severity. The risk to Ontario is currently highly uncertain.

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They next few weeks should tell us if they are genuine contenders for the Omicron throne, and by then, we should know more about their severity, and immune evasion properties. 

Surveillance, testing, and genomic sequencing are limited (and variable) around the country, so Nowcast numbers should be viewed as rough estimates, As we've seen repeatedly already, these weekly numbers are subject to revision.   

The latest CDC Nowcast summary follows:

Due to its ability to continually reinvent itself, the future evolution and impact of COVID remains highly unpredictable. Despite political proclamations to the contrary, our pandemic coronavirus appears to be in no hurry to recede quietly into the night.